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Mehmet Volkan Atalay

Department of Computer Engineering
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iBioProVis: interactive visualization and analysis of compound bioactivity space
Dönmez, Ataberk; Rifaioğlu, Ahmet Süreyya; Acar, Aybar; DOĞAN, TUNCA; Atalay, Rengül; Atalay, Mehmet Volkan (Oxford University Press (OUP), 2020-08-15)
SUMMARY: iBioProVis is an interactive tool for visual analysis of the compound bioactivity space in the context of target proteins, drugs and drug candidate compounds. iBioProVis tool takes target protein identifiers and, ...
Data stream clustering: a review
Zubaroglu, Alaettin; Atalay, Mehmet Volkan (Springer Science and Business Media LLC, 2020-07-01)
Number of connected devices is steadily increasing and these devices continuously generate data streams. Real-time processing of data streams is arousing interest despite many challenges. Clustering is one of the most suit...
DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations
Rifaioğlu, Ahmet Süreyya; Nalbat, Esra; Atalay, Mehmet Volkan; Martin, Maria Jesus; Atalay, Rengül; DOĞAN, TUNCA (2020-03-07)
The identification of physical interactions between drug candidate compounds and target biomolecules is an important process in drug discovery. Since conventional screening procedures are expensive and time consuming, comp...
Forecasting of Product Quality Through Anomaly Detection
Dinç, Mehmet; Ertekin Bolelli, Şeyda; Özkan, Hadi; Meydanlı, Can; Atalay, Mehmet Volkan (2020)
Forecasting of product quality by means of anomaly detection is crucial in real-world applications such as manufacturing systems. In manufacturing systems, the quality is assured through tests performed on sample units ran...
Online embedding and clustering of data streams
Zubaroǧlu, Alaettin; Atalay, Mehmet Volkan (2019-11-20)
© 2019 Association for Computing Machinery.Number of connected devices is steadily increasing and these devices continuously generate data streams. These data streams are often high dimensional and contain concept drift. R...
Comparison of predictive models for forecasting timeseries data
Özen, Serkan; Atalay, Mehmet Volkan; Yazıcı, Adnan (2019-11-20)
© 2019 Association for Computing Machinery.Dramatic increase in data size enabled researchers to study analysis and prediction of big data. Big data can be formed in many ways and one alternative is through the use of sens...
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Zhou, N; Jiang, Y; Bergquist, TR; Lee, AJ; Kacsoh, BZ; Crocker, AW; Lewis, KA; Georghiou, G; Nguyen, HN; Hamid, MN; Davis, L; Dogan, T; Atalay, Mehmet Volkan; Rifaioğlu, Ahmet Süreyya; Dalkıran, A; Atalay, Rengül; Zhang, C; Hurto, RL; Freddolino, PL; et.al. (2019-11-19)
Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the res...
CROssBAR: Comprehensive Resource of Biomedical Relations with Network Representations and Deep Learning
Joshi, Vishal; Doğan, Tunca; Atalay, Rengül; Martin, Maria-Jesus; Saidi, Rabie; Zellner, Hermann; Volynkin, Vladimir; Sinoplu, Esra; Atas, Heval; Nightingale, Andrew; Rifaioğlu, Ahmet Süreyya; Atalay, Mehmet Volkan (2019-07-21)
Biomedical information is scattered across different biological data resources, which are biologically related but only loosely linked to each other in terms of data connections. This hinders the applications of inte...
iBioProVis: Interactive Visualization and Analysis of Compound Bioactivity Space
Dönmez, Ataberk; Rifaioğlu, Ahmet Süreyya; Acar, Aybar Can; Doğan, Tunca; Martin, Maria Jesus; Atalay, Rengül; Atalay, Mehmet Volkan (2019-07-21)
Visualization and interpretation of high-dimensional chemical compound and target space is critical for better understanding of the mechanisms of bioactivity space and drug discovery process. Here, we describe iBio...
DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks
Rifaioğlu, Ahmet Süreyya; Dogan, Tunca; Martin, Maria Jesus; Atalay, Rengül; Atalay, Mehmet Volkan (2019-05-14)
Automated protein function prediction is critical for the annotation of uncharacterized protein sequences, where accurate prediction methods are still required. Recently, deep learning based methods have outperformed conve...